MolNFT v1 · #174713 · protein

The crystal structure of trypanosoma brucei RNase D : cmp complex

7C47 · Cchc-type domain-containing protein: “The crystal structure of trypanosoma brucei RNase D : cmp complex”. X-ray diffraction, 3 ligands (C, ZN, MN), 3 pockets (best druggability 0.55). MolNFT v1 #174713 on GenesisL1: 3D structure…

PDB: 7C47
Type: protein
Length: 295 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cchc-type domain-containing protein
UniProt: Q38DE2
Ligands: C, ZN, MN
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cchc-type domain-containing protein	protein	295	43% helix, 12% strand	Q38DE2

Ligands and binding sites

C · Cytidine-5'-monophosphate · ligand · 2 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	363	0.55	0.74	30	MN
2	83	0.30	0.72	14	empty
3	57	0.30	0.76	16	empty

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

7C47 · The crystal structure of Trypanosoma brucei RNase D : CMP complex · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q38DE2
Elsewhere: RCSB PDB 7C47 · PDBe 7C47 · UniProt Q38DE2

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